1
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Sun F, Qin L, Tang Z, Tang Q. Revisiting the activity origin of the PtAu 24(SR) 18 nanocluster for enhanced electrocatalytic hydrogen evolution by combining first-principles simulations with the experimental in situ FTIR technique. Chem Sci 2024:d4sc04212c. [PMID: 39290593 PMCID: PMC11403574 DOI: 10.1039/d4sc04212c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 09/05/2024] [Indexed: 09/19/2024] Open
Abstract
Thiolate-protected metal nanoclusters (NCs) have been widely used in various electrocatalytic reactions, yet the dynamic evolution of metal NCs during electrocatalysis has been rarely explored and the activity origin remains largely ambiguous. Herein, using a PtAu24(SCH3)18 NC as a prototype model, we combined advanced first-principles calculations and attenuated total reflection surface-enhanced infrared spectroscopy (ATR-SEIRAS) to re-examine its active site and reaction dynamics in the hydrogen evolution reaction (HER). It has been previously assumed that the central Pt is the only catalytic center. However, differently, we observed the spontaneous desorption of thiolate ligands under moderate potential, and the dethiolated PtAu24 exhibits excellent HER activity, which is contributed not only by the central Pt atom but also by the exposed bridged Au sites. Particularly, the exposed Au exhibits high activity even comparable to Pt, and the synergistic effect between them makes dethiolated PtAu24 an extraordinary HER electrocatalyst, even surpassing the commercial Pt/C catalyst. Our predictions are further verified by electrochemical activation experiments and in situ FTIR (ATR-SEIRAS) characterization, where evident adsorption of Au-H* and Pt-H* bonds is monitored. This work detected, for the first time, the Au-S interfacial dynamics of the PtAu24 nanocluster in electrocatalytic processes, and quantitatively evaluated the essential catalytic role of the exposed Au sites that has been largely overlooked in previous studies.
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Affiliation(s)
- Fang Sun
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Chemical Theory and Mechanism, Chongqing University Chongqing 401331 China
| | - Lubing Qin
- New Energy Research Institute, School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Center Guangzhou 510006 China
| | - Zhenghua Tang
- New Energy Research Institute, School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Center Guangzhou 510006 China
| | - Qing Tang
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Chemical Theory and Mechanism, Chongqing University Chongqing 401331 China
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2
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Sun F, Qin L, Tang Z, Deng G, Bootharaju MS, Wei Z, Tang Q, Hyeon T. -SR removal or -R removal? A mechanistic revisit on the puzzle of ligand etching of Au 25(SR) 18 nanoclusters during electrocatalysis. Chem Sci 2023; 14:10532-10546. [PMID: 37800008 PMCID: PMC10548520 DOI: 10.1039/d3sc03018k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/09/2023] [Indexed: 10/07/2023] Open
Abstract
Accurate identification of active sites is highly desirable for elucidation of the reaction mechanism and development of efficient catalysts. Despite the promising catalytic performance of thiolated metal nanoclusters (NCs), their actual catalytic sites remain elusive. Traditional first-principles calculations and experimental observations suggested dealkylated S and dethiolated metal, respectively, to be the active centers. However, the real kinetic origin of thiolate etching during the electrocatalysis of NCs is still puzzling. Herein, we conducted advanced first-principles calculations and electrochemical/spectroscopic experiments to unravel the electrochemical etching kinetics of thiolate ligands in prototype Au25(SCH3)18 NC. The electrochemical processes are revealed to be spontaneously facilitated by dethiolation (i.e., desorption of -SCH3), forming the free HSCH3 molecule after explicitly including the solvent effect and electrode potential. Thus, exposed under-coordinated Au atoms, rather than the S atoms, serve as the real catalytic sites. The thermodynamically preferred Au-S bond cleavage arises from the selective attack of H from proton/H2O on the S atom under suitable electrochemical bias due to the spatial accessibility and the presence of S lone pair electrons. Decrease of reduction potential promotes the proton attack on S and significantly accelerates the kinetics of Au-S bond breakage irrespective of the pH of the medium. Our theoretical results are further verified by the experimental electrochemical and spectroscopic data. At more negative electrode potentials, the number of -SR ligands decreased with concomitant increase of the vibrational intensity of S-H bonds. These findings together clarify the atomic-level activation mechanism on the surface of Au25(SR)18 NCs.
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Affiliation(s)
- Fang Sun
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University Chongqing 401331 China
| | - Lubing Qin
- New Energy Research Institute, School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Center Guangzhou 510006 China
| | - Zhenghua Tang
- New Energy Research Institute, School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Center Guangzhou 510006 China
| | - Guocheng Deng
- Center for Nanoparticle Research, Institute for Basic Science (IBS) Seoul 08826 Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
| | - Megalamane S Bootharaju
- Center for Nanoparticle Research, Institute for Basic Science (IBS) Seoul 08826 Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
| | - Zidong Wei
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University Chongqing 401331 China
| | - Qing Tang
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University Chongqing 401331 China
| | - Taeghwan Hyeon
- Center for Nanoparticle Research, Institute for Basic Science (IBS) Seoul 08826 Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
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3
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Haque S, Chatterjee A. Thermodynamic calculations using reverse Monte Carlo: Simultaneously tuning multiple short-range order parameters for 2D lattice adsorption problem. J Chem Phys 2023; 159:104106. [PMID: 37694750 DOI: 10.1063/5.0165182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Lattice simulations are an important class of problems in crystalline solids, surface science, alloys, adsorption, absorption, separation, catalysis, to name a few. We describe a fast computational method for performing lattice thermodynamic calculations that is based on the use of the reverse Monte Carlo (RMC) technique and multiple short-range order (SRO) parameters. The approach is comparable in accuracy to the Metropolis Monte Carlo (MC) method. The equilibrium configuration is determined in 5-10 Newton-Raphson iterations by solving a system of coupled nonlinear algebraic SRO growth rate equations. This makes the RMC-based method computationally more efficient than MC, given that MC typically requires sampling of millions of configurations. The technique is applied to the interacting 2D adsorption problem. Unlike grand canonical MC, RMC is found to be adept at tackling geometric frustration, as it is able to quickly and correctly provide the ordered c(2 × 2) adlayer configuration for Cl adsorbed on a Cu (100) surface.
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Affiliation(s)
- Suhail Haque
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Abhijit Chatterjee
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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4
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Kumar A, Chatterjee A. A probabilistic microkinetic modeling framework for catalytic surface reactions. J Chem Phys 2023; 158:024109. [PMID: 36641399 DOI: 10.1063/5.0132877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We present a probabilistic microkinetic modeling (MKM) framework that incorporates the short-ranged order (SRO) evolution for adsorbed species (adspecies) on a catalyst surface. The resulting model consists of a system of ordinary differential equations. Adsorbate-adsorbate interactions, surface diffusion, adsorption, desorption, and catalytic reaction processes are included. Assuming that the adspecies ordering/arrangement is accurately described by the SRO parameters, we employ the reverse Monte Carlo (RMC) method to extract the relevant local environment probability distributions and pass them to the MKM. The reaction kinetics is faithfully captured as accurately as the kinetic Monte Carlo (KMC) method but with a computational time requirement of few seconds on a standard desktop computer. KMC, on the other hand, can require several days for the examples discussed. The framework presented here is expected to provide the basis for wider application of the RMC-MKM approach to problems in computational catalysis, electrocatalysis, and material science.
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Affiliation(s)
- Aditya Kumar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Abhijit Chatterjee
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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5
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Qian SJ, Cao H, Chen JW, Chen JC, Wang YG, Li J. Critical Role of Explicit Inclusion of Solvent and Electrode Potential in the Electrochemical Description of Nitrogen Reduction. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sheng-Jie Qian
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Hao Cao
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Jie-Wei Chen
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Jun-Chi Chen
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Yang-Gang Wang
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Jun Li
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
- Department of Chemistry, Tsinghua University and Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Beijing 100084, China
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6
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Sahle CJ, de Clermont Gallerande E, Niskanen J, Longo A, Elbers M, Schroer MA, Sternemann C, Jahn S. Hydration in aqueous NaCl. Phys Chem Chem Phys 2022; 24:16075-16084. [PMID: 35735165 DOI: 10.1039/d2cp00162d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atomistic details about the hydration of ions in aqueous solutions are still debated due to the disordered and statistical nature of the hydration process. However, many processes from biology, physical chemistry to materials sciences rely on the complex interplay between solute and solvent. Oxygen K-edge X-ray excitation spectra provide a sensitive probe of the local atomic and electronic surrounding of the excited sites. We used ab initio molecular dynamics simulations together with extensive spectrum calculations to relate the features found in experimental oxygen K-edge spectra of a concentration series of aqueous NaCl with the induced structural changes upon solvation of the salt and distill the spectral fingerprints of the first hydration shells around the Na+- and Cl--ions. By this combined experimental and theoretical approach, we find the strongest spectral changes to indeed result from the first hydration shells of both ions and relate the observed shift of spectral weight from the post- to the main-edge to the origin of the post-edge as a shape resonance.
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Affiliation(s)
- Christoph J Sahle
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, CS40220, FR-38043 Grenoble Cedex 9, France.
| | | | - Johannes Niskanen
- Department of Physics and Astronomy, University of Turku, FI-20014 Turun Yliopisto, Finland
| | - Alessandro Longo
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, CS40220, FR-38043 Grenoble Cedex 9, France.
| | - Mirko Elbers
- Fakultät Physik/DELTA, Technische Universität Dortmund, D-44221 Dortmund, Germany
| | - Martin A Schroer
- Nanoparticle Process Technology, University of Duisburg-Essen, D-47057 Duisburg, Germany
| | - Christian Sternemann
- Fakultät Physik/DELTA, Technische Universität Dortmund, D-44221 Dortmund, Germany
| | - Sandro Jahn
- Institute of Geology and Mineralogy, University of Cologne, D-50674 Köln, Germany
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7
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Cao H, Zhang Z, Chen JW, Wang YG. Potential-Dependent Free Energy Relationship in Interpreting the Electrochemical Performance of CO 2 Reduction on Single Atom Catalysts. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01470] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hao Cao
- Shenzhen Key Laboratory of Energy Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zisheng Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Jie-Wei Chen
- Shenzhen Key Laboratory of Energy Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yang-Gang Wang
- Shenzhen Key Laboratory of Energy Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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8
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Agrahari G, Chatterjee A. Thermodynamic calculations using reverse Monte Carlo: convergence aspects, sources of error and guidelines for improving accuracy. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2072497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Gargi Agrahari
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Abhijit Chatterjee
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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9
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Chen JW, Zhang Z, Yan HM, Xia GJ, Cao H, Wang YG. Pseudo-adsorption and long-range redox coupling during oxygen reduction reaction on single atom electrocatalyst. Nat Commun 2022; 13:1734. [PMID: 35365615 PMCID: PMC8975818 DOI: 10.1038/s41467-022-29357-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 03/10/2022] [Indexed: 11/23/2022] Open
Abstract
Fundamental understanding of the dynamic behaviors at the electrochemical interface is crucial for electrocatalyst design and optimization. Here, we revisit the oxygen reduction reaction mechanism on a series of transition metal (M = Fe, Co, Ni, Cu) single atom sites embedded in N-doped nanocarbon by ab initio molecular dynamics simulations with explicit solvation. We have identified the dissociative pathways and the thereby emerged solvated hydroxide species for all the proton-coupled electron transfer (PCET) steps at the electrochemical interface. Such hydroxide species can be dynamically confined in a "pseudo-adsorption" state at a few water layers away from the active site and respond to the redox event at the catalytic center in a coupled manner within timescale less than 1 ps. In the PCET steps, the proton species (in form of hydronium in neutral/acidic media or water in alkaline medium) can protonate the pseudo-adsorbed hydroxide without needing to travel to the direct catalyst surface. This, therefore, expands the reactive region beyond the direct catalyst surface, boosting the reaction kinetics via alleviating mass transfer limits. Our work implies that in catalysis the reaction species may not necessarily bind to the catalyst surface but be confined in an active region.
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Affiliation(s)
- Jie-Wei Chen
- Department of Chemistry, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Zisheng Zhang
- Department of Chemistry, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Hui-Min Yan
- Department of Chemistry, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Guang-Jie Xia
- Department of Chemistry, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Hao Cao
- Department of Chemistry, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Yang-Gang Wang
- Department of Chemistry, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
- Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
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10
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Terban MW, Billinge SJL. Structural Analysis of Molecular Materials Using the Pair Distribution Function. Chem Rev 2022; 122:1208-1272. [PMID: 34788012 PMCID: PMC8759070 DOI: 10.1021/acs.chemrev.1c00237] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 12/16/2022]
Abstract
This is a review of atomic pair distribution function (PDF) analysis as applied to the study of molecular materials. The PDF method is a powerful approach to study short- and intermediate-range order in materials on the nanoscale. It may be obtained from total scattering measurements using X-rays, neutrons, or electrons, and it provides structural details when defects, disorder, or structural ambiguities obscure their elucidation directly in reciprocal space. While its uses in the study of inorganic crystals, glasses, and nanomaterials have been recently highlighted, significant progress has also been made in its application to molecular materials such as carbons, pharmaceuticals, polymers, liquids, coordination compounds, composites, and more. Here, an overview of applications toward a wide variety of molecular compounds (organic and inorganic) and systems with molecular components is presented. We then present pedagogical descriptions and tips for further implementation. Successful utilization of the method requires an interdisciplinary consolidation of material preparation, high quality scattering experimentation, data processing, model formulation, and attentive scrutiny of the results. It is hoped that this article will provide a useful reference to practitioners for PDF applications in a wide realm of molecular sciences, and help new practitioners to get started with this technique.
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Affiliation(s)
- Maxwell W. Terban
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Simon J. L. Billinge
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Condensed
Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, New York 11973, United States
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11
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Reich V, Majumdar A, Müller M, Busch S. Comparison of molecular dynamics simulations of water with neutron and X-ray scattering experiments. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202227201015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The atomistic structure and dynamics obtained from molecular dynamics (MD) simulations with the example of TIP3P (rigid and flexible) and TIP4P/2005 (rigid) water is compared to neutron and X-ray scattering data at ambient conditions. Neutron and X-ray diffractograms are calculated from the simulations for four isotopic substitutions as well as the incoherent intermediate scattering function for neutrons. The resulting curves are compared to each other and to published experimental data. Differences between simulated and measured intermediate scattering functions are quantified by fitting an analytic model to the computed values. The sensitivity of the scattering curves to the parameters of the MD simulations is demonstrated on the example of two parameters, bond length and angle.
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12
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Cuny J, Cerda Calatayud J, Ansari N, Hassanali AA, Rapacioli M, Simon A. Simulation of Liquids with the Tight-Binding Density-Functional Approach and Improved Atomic Charges. J Phys Chem B 2020; 124:7421-7432. [PMID: 32696649 DOI: 10.1021/acs.jpcb.0c04167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Theoretical description of liquids, especially liquid water, is an ongoing subject with important implications in various domains such as homogeneous catalysis; solvation of molecular, ionic, and biomolecular species; and reactivity. Various formalisms exist to describe liquids, each one displaying its own balance between accuracy and computational cost that defines its range of applications. The present article revisits the ability of the density-functional-based tight-binding (SCC-DFTB) approach to model liquids by focusing on liquid water and liquid benzene under ambient conditions. To do so, we benchmark a recent correction for the SCC-DFTB atomic charges that allows for a drastic improvement of the pair radial distribution functions of liquid water as compared to both experimental data and density-functional theory results performed in the generalized-gradient approximation. We also report the coupling of the deMonNano and i-PI codes to perform path-integral molecular dynamics. This allows us to rationalize the impact of nuclear quantum effects on the SCC-DFTB description of liquid water. This study evidences the rather good ability of SCC-DFTB to describe liquid water and liquid benzene. As the first example of application, we also present results for a benzene molecule solvated in water with the perspectives of further studies devoted to solvent/water interfaces.
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Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jesus Cerda Calatayud
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Narjes Ansari
- The Abdus Salam International Center for Theoretical Physics, Condensed Matter and Statistical Physics Section, Strada Costiera 11, 34151 Trieste, Italy.,Department of Chemistry and Applied Biosciences, ETH Zurich, 3 c/o USI Campus, Via Giuseppe Buffi13, 6900 Lugano, Switzerland.,Facoltà di informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Ali A Hassanali
- The Abdus Salam International Center for Theoretical Physics, Condensed Matter and Statistical Physics Section, Strada Costiera 11, 34151 Trieste, Italy
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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13
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Lourenço MP, dos Santos EC, Pettersson LGM, Duarte HA. Accurate SCC-DFTB Parametrization for Bulk Water. J Chem Theory Comput 2020; 16:1768-1778. [DOI: 10.1021/acs.jctc.9b00816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Maicon Pierre Lourenço
- Departamento de Quı́mica e Fı́sica−Centro de Ciências Exatas, Naturais e da Saúde (CCENS), Universidade Federal do Espı́rito Santo, 29500-000, Alegre, Espı́rito Santo Brasil
| | - Egon Campos dos Santos
- Departamento de Quı́mica, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Minas Gerais Brasil
- Department of Physics, AlbaNova University Center, Stockholm University, S-10691 Stockholm, Sweden
| | - Lars G. M. Pettersson
- Department of Physics, AlbaNova University Center, Stockholm University, S-10691 Stockholm, Sweden
| | - Hélio Anderson Duarte
- Departamento de Quı́mica, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Minas Gerais Brasil
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14
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Monroe JI, Shell MS. Decoding signatures of structure, bulk thermodynamics, and solvation in three-body angle distributions of rigid water models. J Chem Phys 2019; 151:094501. [PMID: 31492058 DOI: 10.1063/1.5111545] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A tetrahedral structure resulting from hydrogen bonding is a hallmark of liquid water and plays a significant role in determining its unique thermophysical properties. This water feature has helped understand anomalous properties and physically interpret and model hydrophobic solvation thermodynamics. Tetrahedrality is well described by the geometric relationship of any central water molecule with two of its nearest neighbors in the first coordination shell, as defined by the corresponding "three-body" angle. While order parameters and even full water models have been developed using specific or average features of the three-body angle distribution, here we examine the distribution holistically, tracking its response to changes in temperature, density, and the presence of model solutes. Surprisingly, we find that the three-body distribution responds by varying primarily along a single degree of freedom, suggesting a remarkably simplified view of water structure. We characterize three-body angle distributions across temperature and density space and identify principal components of the variations with state conditions. We show that these principal components embed physical significance and trace out transitions between tetrahedral and simple-fluid-like behavior. Moreover, we find that the ways three-body angles vary within the hydration shells of model colloids of different types and sizes are nearly identical to the variations seen in bulk water across density and temperature. Importantly, through the principal directions of these variations, we find that perturbations to the hydration-water distributions well predict the thermodynamics associated with colloid solvation, in particular, the relative entropy of this process that captures indirect, solvent-mediated contributions to the hydration free energy.
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Affiliation(s)
- Jacob I Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-9010, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-9010, USA
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15
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Affiliation(s)
- C. Shi
- State Key Laboratory of Advanced Special Steel, Shanghai Key Laboratory of Advanced Ferrometallurgy, and School of Materials Science and Engineering, Shanghai University, Shanghai, People’s Republic of China
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | | | - C. J. Benmore
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
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16
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Pathak H, Späh A, Kim KH, Tsironi I, Mariedahl D, Blanco M, Huotari S, Honkimäki V, Nilsson A. Intermediate range O-O correlations in supercooled water down to 235 K. J Chem Phys 2019; 150:224506. [PMID: 31202250 DOI: 10.1063/1.5100811] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Wide angle x-ray scattering of supercooled water down to 234.8 K was studied using high energy x rays at the European Synchrotron Radiation Facility. The oxygen-oxygen pair distribution function (PDF) was calculated from the scattering pattern out to the 5th peak at an intermolecular distance, r ≈ 11 Å. We observe that the 4th peak and the 5th peak in the PDF increase in height upon supercooling. We also observe that the 4th peak position (r4) shifts to shorter distances upon supercooling consistent with previous studies, but we see a more rapid change at the lowest temperature. The running oxygen-oxygen coordination number is calculated for 5 different temperatures, and an isosbestic point at riso = 3.31 ± 0.05 Å was found corresponding to a coordination number of 4.39 ± 0.15. The comparison of the PDF of the coldest water with that of amorphous ice shows distinct differences. We propose that there are 5-member pentamer rings in low density liquid-like structures giving rise to the sharp correlations at r ≈ 9 Å and r ≈ 11 Å.
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Affiliation(s)
- Harshad Pathak
- Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 Stockholm, Sweden
| | - Alexander Späh
- Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 Stockholm, Sweden
| | - Kyung Hwan Kim
- Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 Stockholm, Sweden
| | - Ifigeneia Tsironi
- Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 Stockholm, Sweden
| | - Daniel Mariedahl
- Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 Stockholm, Sweden
| | - Maria Blanco
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Simo Huotari
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Veijo Honkimäki
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Anders Nilsson
- Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 Stockholm, Sweden
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17
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Affiliation(s)
- Chris Benmore
- Advanced Photon Source, Argonne National Laboratory, Lemont, USA
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18
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Zhovtobriukh I, Norman P, Pettersson LGM. X-ray absorption spectrum simulations of hexagonal ice. J Chem Phys 2019; 150:034501. [DOI: 10.1063/1.5078385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Iurii Zhovtobriukh
- FYSIKUM, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Lars G. M. Pettersson
- FYSIKUM, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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19
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Pettersson LGM. A Two-State Picture of Water and the Funnel of Life. SPRINGER PROCEEDINGS IN PHYSICS 2019. [DOI: 10.1007/978-3-030-21755-6_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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20
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Kameda Y, Amo Y, Usuki T, Umebayashi Y, Ikeda K, Otomo T. Neutron Diffraction Study on Partial Pair Correlation Functions of Water at Ambient Temperature. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuo Kameda
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Yuko Amo
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Takeshi Usuki
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Yasuhiro Umebayashi
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Kazutaka Ikeda
- Institute of Material Structure Science, KEK, Tsukuba, Ibaraki 305-080, Japan
| | - Toshiya Otomo
- Institute of Material Structure Science, KEK, Tsukuba, Ibaraki 305-080, Japan
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21
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Khatua P, Bandyopadhyay S. Understanding the microscopic origin behind heterogeneous properties of water confined in and around A β17-42 protofilaments. J Chem Phys 2018; 149:065101. [PMID: 30111136 DOI: 10.1063/1.5040672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aggregation of amyloid beta (Aβ) peptides in the brain is responsible for one of the most devastating neurodegenerative diseases, namely, Alzheimer's disease. In this study, we have carried out atomistic molecular dynamics simulations to explore the effects of non-uniform structural distortions of Aβ17-42 pre-fibrillar aggregates of different sizes on the microscopic structure and ordering of water molecules confined within their amphiphilic nanocores. The calculations revealed non-uniform peptide-water interactions resulting in simultaneous existence of both highly ordered and disordered water molecules within the spatially heterogeneous confined environment of the protofilament cores. It is found that the high degree of ordering originates from a sizable fraction of doubly coordinated core water molecules, while the randomly oriented ones are those that are coordinated with three neighbors in their first coordination shells. Furthermore, it is quantitatively demonstrated that relative fractions of these two types of water molecules are correlated with the protofilament core topology and the degree of confinement within that. It is proposed that the ordered core waters are likely to stabilize the Aβ protofilaments by screening the residue charges and favoring water-mediated salt bridge formations, while the randomly oriented ones can drive further growth of the protofilaments by being displaced easily during the docking of additional peptides. In that way, both types of core water molecules can play equally important roles in controlling the growth and stability of the Aβ-aggregates.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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22
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Chang R, Asatyas S, Lkhamsuren G, Hirohara M, Mondarte EAQ, Suthiwanich K, Sekine T, Hayashi T. Water near bioinert self-assembled monolayers. Polym J 2018. [DOI: 10.1038/s41428-018-0075-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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23
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Galamba N, Cabral BJC. Magnetic properties and core electron binding energies of liquid water. J Chem Phys 2018; 148:044510. [PMID: 29390846 DOI: 10.1063/1.5011037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The magnetic properties and the core and inner valence electron binding energies of liquid water are investigated. The adopted methodology relies on the combination of molecular dynamics and electronic structure calculations. Born-Oppenheimer molecular dynamics with the Becke and Lee-Yang-Parr functionals for exchange and correlation, respectively, and includes an empirical correction (BLYP-D3) functional and classical molecular dynamics with the TIP4P/2005-F model were carried out. The Keal-Tozer functional was applied for predicting magnetic shielding and spin-spin coupling constants. Core and inner valence electron binding energies in liquid water were calculated with symmetry adapted cluster-configuration interaction. The relationship between the magnetic shielding constant σ(17O), the role played by the oxygen atom as a proton acceptor and donor, and the tetrahedral organisation of liquid water are investigated. The results indicate that the deshielding of the oxygen atom in water is very dependent on the order parameter (q) describing the tetrahedral organisation of the hydrogen bond network. The strong sensitivity of magnetic properties on changes of the electronic density in the nuclei environment is illustrated by a correlation between σ(17O) and the energy gap between the 1a1[O1s] (core) and the 2a1 (inner valence) orbitals of water. Although several studies discussed the eventual connection between magnetic properties and core electron binding energies, such a correlation could not be clearly established. Here, we demonstrate that for liquid water this correlation exists although involving the gap between electron binding energies of core and inner valence orbitals.
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Affiliation(s)
- N Galamba
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Edifício C8, Campo Grande, 1749-016 Lisboa, Portugal
| | - Benedito J C Cabral
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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24
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Onufriev AV, Izadi S. Water models for biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1347] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexey V. Onufriev
- Department of Physics; Virginia Tech; Blacksburg VA USA
- Department of Computer Science; Virginia Tech; Blacksburg VA USA
- Center for Soft Matter and Biological Physics; Virginia Tech; Blacksburg VA USA
| | - Saeed Izadi
- Early Stage Pharmaceutical Development; Genentech Inc.; South San Francisco, CA USA
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25
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Dhabal D, Wikfeldt KT, Skinner LB, Chakravarty C, Kashyap HK. Probing the triplet correlation function in liquid water by experiments and molecular simulations. Phys Chem Chem Phys 2017; 19:3265-3278. [DOI: 10.1039/c6cp07599a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three-body information of liquid water is extracted using X-ray diffraction experiment as well as in molecular simulations via isothermal pressure derivative of structure factor term.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi
- India
| | | | | | | | - Hemant K. Kashyap
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi
- India
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26
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Morozenko A, Stuchebrukhov AA. Dowser++, a new method of hydrating protein structures. Proteins 2016; 84:1347-57. [PMID: 27273373 DOI: 10.1002/prot.25081] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/19/2016] [Accepted: 05/30/2016] [Indexed: 12/30/2022]
Abstract
A new method of hydrating protein structures, which we call Dowser++, is presented. The method is based on a semi-empirical modification of a popular program for protein hydration Dowser, and the usage of protocols AutoDock Vina, and WaterDock. The positions of water molecules predicted by Dowser++ were compared with experimental data for a set of 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules, as well as for the D- and K-channels of cytochrome c oxidase, and the recent data on PSII. Comparison is also made with the predictions of the original Dowser, and its improved version, Dowser+, described in our previous publication. We also present a model for quantitative estimation of the quality of water molecules placement made by a program, which includes an assumption of possible false negative data from the crystallographic analysis. The comparison of predictions made by Dowser++, Dowser and Dowser+ demonstrates significant improvement of predictive power of the new method. Proteins 2016; 84:1347-1357. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- A Morozenko
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California, 95616.
| | - A A Stuchebrukhov
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California, 95616.
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27
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Dhabal D, Nguyen AH, Singh M, Khatua P, Molinero V, Bandyopadhyay S, Chakravarty C. Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids. J Chem Phys 2015; 143:164512. [DOI: 10.1063/1.4933420] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Debdas Dhabal
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Andrew Huy Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Murari Singh
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Prabir Khatua
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Valeria Molinero
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Sanjoy Bandyopadhyay
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
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28
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Sánchez-Gil V, Noya E, Temleitner L, Pusztai L. Reverse Monte Carlo modeling: The two distinct routes of calculating the experimental structure factor. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.02.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Huang YL, Zhang X, Ma Z, Zhou G, Sun CQ, Gong YY. Potential Paths for the Hydrogen-Bond Relaxing With (H 2O) NCluster Size. J Phys Chem A 2015. [DOI: 10.1021/acs.jpca.5b03921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Huang YL, Zhang X, Ma Z, Zhou G, Sun CQ, Gong YY. Potential Paths for the Hydrogen-Bond Relaxing With (H 2O) N Cluster Size. J Phys Chem A 2015; 119:16962-16971. [PMID: 26119068 DOI: 10.1021/acs.jpcc.5b03921] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Relaxation of the inter- and intra-molecular interactions for the hydrogen bond (O:H-O) between undercoordinated molecules determines the unusual behavior of water nanodroplets and nanobubbles. However, probing such potentials remains unreality. Here we show that the Lagrangian solution [Huang et al., J. Phys. Chem. B, 2013. 117: 13639] transforms the observed H-O bond (x = H) and O:H nonbond (x = L) lengths and phonon frequencies (dx, x) [Sun et al., J. Phys. Chem. Lett., 2013. 4: 2565] into the respective force constants and bond energies (kx, Ex) and hence enables the mapping of the potential paths for the O:H-O bond relaxing with water cluster size. Results show that molecular undercoordination not only reduces the molecular size (dH) with enhanced H-O energy from the bulk value of 3.97 to 5.10 eV for a H2O monomer, but also enlarges the molecular separation (dL) with reduced O:H energy from 95 to 35 meV for a dimer. The H-O energy gain raises the melting point from bulk value 273 to 310 K for the skin and the O:H energy loss lowers the freezing temperature from bulk value 258 to 202 K for 1.4 nm sized droplet, by dispersing the quasisolid phase boundaries.
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31
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Dhabal D, Singh M, Wikfeldt KT, Chakravarty C. Triplet correlation functions in liquid water. J Chem Phys 2015; 141:174504. [PMID: 25381528 DOI: 10.1063/1.4898755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Triplet correlations have been shown to play a crucial role in the transformation of simple liquids to anomalous tetrahedral fluids [M. Singh, D. Dhabal, A. H. Nguyen, V. Molinero, and C. Chakravarty, Phys. Rev. Lett. 112, 147801 (2014)]. Here we examine triplet correlation functions for water, arguably the most important tetrahedral liquid, under ambient conditions, using configurational ensembles derived from molecular dynamics (MD) simulations and reverse Monte Carlo (RMC) datasets fitted to experimental scattering data. Four different RMC data sets with widely varying hydrogen-bond topologies fitted to neutron and x-ray scattering data are considered [K. T. Wikfeldt, M. Leetmaa, M. P. Ljungberg, A. Nilsson, and L. G. M. Pettersson, J. Phys. Chem. B 113, 6246 (2009)]. Molecular dynamics simulations are performed for two rigid-body effective pair potentials (SPC/E and TIP4P/2005) and the monatomic water (mW) model. Triplet correlation functions are compared with other structural measures for tetrahedrality, such as the O-O-O angular distribution function and the local tetrahedral order distributions. In contrast to the pair correlation functions, which are identical for all the RMC ensembles, the O-O-O triplet correlation function can discriminate between ensembles with different degrees of tetrahedral network formation with the maximally symmetric, tetrahedral SYM dataset displaying distinct signatures of tetrahedrality similar to those obtained from atomistic simulations of the SPC/E model. Triplet correlations from the RMC datasets conform closely to the Kirkwood superposition approximation, while those from MD simulations show deviations within the first two neighbour shells. The possibilities for experimental estimation of triplet correlations of water and other tetrahedral liquids are discussed.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Murari Singh
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
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32
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33
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TOKUSHIMA T. 1. 軟X線分光が見た水の液体構造. ELECTROCHEMISTRY 2014. [DOI: 10.5796/electrochemistry.82.756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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34
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Pardo LC, Henao A, Busch S, Guàrdia E, Tamarit JL. A continuous mixture of two different dimers in liquid water. Phys Chem Chem Phys 2014; 16:24479-83. [DOI: 10.1039/c4cp03664f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Liquid water is formed by a continuous mixture of two different dimers (cis and trans) with distinct energies related to different relative water molecule orientations.
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Affiliation(s)
- L. C. Pardo
- Grup de Caracterització de Materials
- Departament de Física i Enginyeria Nuclear
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona, Spain
| | - A. Henao
- Grup de Caracterització de Materials
- Departament de Física i Enginyeria Nuclear
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona, Spain
| | - S. Busch
- Laboratory of Molecular Biophysics
- Department of Biochemistry
- University of Oxford
- Oxford OX1 3QU, UK
| | - E. Guàrdia
- Grup de Simulació per Ordinador en Matèria Condensada
- Departament de Física i Enginyeria Nuclear
- B4-B5 Campus Nord
- Universitat Politècnica de Catalunya
- E-08034 Barcelona, Spain
| | - J. Ll. Tamarit
- Grup de Caracterització de Materials
- Departament de Física i Enginyeria Nuclear
- ETSEIB
- Universitat Politècnica de Catalunya
- E-08028 Barcelona, Spain
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35
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Huang Y, Ma Z, Zhang X, Zhou G, Zhou Y, Sun CQ. Hydrogen Bond Asymmetric Local Potentials in Compressed Ice. J Phys Chem B 2013; 117:13639-45. [PMID: 24090472 DOI: 10.1021/jp407836n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Yongli Huang
- Key
Laboratory of Low-dimensional Materials and Application Technology
(Ministry of Education) and Faculty of Materials, Optoelectronics
and Physics, Xiangtan University, Xiangtan 411105, China
| | - Zengsheng Ma
- Key
Laboratory of Low-dimensional Materials and Application Technology
(Ministry of Education) and Faculty of Materials, Optoelectronics
and Physics, Xiangtan University, Xiangtan 411105, China
| | - Xi Zhang
- NOVITAS,
School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798
- Center
for Coordination Bond and Electronic Engineering, College of Materials
Science and Engineering, China Jiliang University, Hangzhou 310018, China
| | - Guanghui Zhou
- Department
of Physics and Key Laboratory for Low-Dimensional Structures and Quantum
Manipulation (Ministry of Education), Hunan Normal University, Changsha 410081, China
| | - Yichun Zhou
- Key
Laboratory of Low-dimensional Materials and Application Technology
(Ministry of Education) and Faculty of Materials, Optoelectronics
and Physics, Xiangtan University, Xiangtan 411105, China
| | - Chang Q. Sun
- Key
Laboratory of Low-dimensional Materials and Application Technology
(Ministry of Education) and Faculty of Materials, Optoelectronics
and Physics, Xiangtan University, Xiangtan 411105, China
- NOVITAS,
School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798
- Center
for Coordination Bond and Electronic Engineering, College of Materials
Science and Engineering, China Jiliang University, Hangzhou 310018, China
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36
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Skinner LB, Huang C, Schlesinger D, Pettersson LGM, Nilsson A, Benmore CJ. Benchmark oxygen-oxygen pair-distribution function of ambient water from x-ray diffraction measurements with a wide Q-range. J Chem Phys 2013; 138:074506. [DOI: 10.1063/1.4790861] [Citation(s) in RCA: 349] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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37
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Kühne TD, Khaliullin RZ. Electronic signature of the instantaneous asymmetry in the first coordination shell of liquid water. Nat Commun 2013; 4:1450. [DOI: 10.1038/ncomms2459] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 01/04/2013] [Indexed: 12/30/2022] Open
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38
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Wikfeldt KT, Batista ER, Vila FD, Jónsson H. A transferable H2O interaction potential based on a single center multipole expansion: SCME. Phys Chem Chem Phys 2013; 15:16542-56. [DOI: 10.1039/c3cp52097h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Khaliullin RZ, Kühne TD. Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies. Phys Chem Chem Phys 2013; 15:15746-66. [DOI: 10.1039/c3cp51039e] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ono J, Ando K. Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets. J Chem Phys 2012; 137:174503. [DOI: 10.1063/1.4762840] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Kale S, Herzfeld J. Natural polarizability and flexibility via explicit valency: the case of water. J Chem Phys 2012; 136:084109. [PMID: 22380034 DOI: 10.1063/1.3688228] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
As the dominant physiological solvent, water drives the folding of biological macromolecules, influences conformational changes, determines the ionization states of surface groups, actively participates in catalytic events, and provides "wires" for long-range proton transfer. Elucidation of all these roles calls for atomistic simulations. However, currently available methods do not lend themselves to efficient simulation of proton transfer events, or even polarizability and flexibility. Here, we report that an explicit account of valency can provide a unified description for the polarizability, flexibility, and dissociability of water in one intuitive and efficient setting. We call this approach LEWIS, after the chemical theory that inspires the use of valence electron pairs. In this paper, we provide details of the method, the choice of the training set, and predictions for the neat ambient liquid, with emphasis on structure, dynamics, and polarization. LEWIS water provides a good description of bulk properties, and dipolar and quadrupolar responses.
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Affiliation(s)
- Seyit Kale
- Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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Li X, Murthy NS, Latour RA. The Structure of Hydrated Poly (D, L - Lactic Acid) Studied With X-Ray Diffraction and Molecular Simulation Methods. Macromolecules 2012; 45:4896-4906. [PMID: 22707795 PMCID: PMC3374654 DOI: 10.1021/ma3004778] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of hydration on the molecular structure of amorphous poly (D, L-lactic acid) (PDLLA) with 50:50 L-to-D ratio has been studied by combining experiments with molecular simulations. X-ray diffraction measurements revealed significant changes upon hydration in the structure functions of the copolymer. Large changes in the structure functions at ~ 10 days of incubation coincided with the large increase in the water uptake from ~1 to ~40% and the formation of voids in the film. Computer modeling based on the recently developed TIGER2/TIGER3 mixed sampling scheme was used to interpret these changes by efficiently equilibrating both dry and hydrated models of PDLLA. Realistic models of bulk amorphous PDLLA structure were generated as demonstrated by close agreement between the calculated and the experimental structure functions. These molecular simulations were used to identify the interactions between water and the polymer at the atomic level including the change of positional order between atoms in the polymer due to hydration. Changes in the partial O-O structure functions, about 95% of which were due to water-polymer interactions, were apparent in the radial distribution functions. These changes, and somewhat smaller changes in the C-C and C-O partial structure functions, clearly demonstrated the ability of the model to capture the hydrogen bonding interactions between water and the polymer, with the probability of water forming hydrogen bonds with the carbonyl oxygen of the ester group being about four times higher than with its ether oxygen.
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Affiliation(s)
- Xianfeng Li
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - N. Sanjeeva Murthy
- New Jersey Center for Biomaterials, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Robert A. Latour
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
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Park K, Lin W, Paesani F. A Refined MS-EVB Model for Proton Transport in Aqueous Environments. J Phys Chem B 2011; 116:343-52. [DOI: 10.1021/jp208946p] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kyoyeon Park
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Wei Lin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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46
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Marčelja S. Hydration forces near charged interfaces in terms of effective ion potentials. Curr Opin Colloid Interface Sci 2011. [DOI: 10.1016/j.cocis.2011.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Pylkkänen T, Sakko A, Hakala M, Hämäläinen K, Monaco G, Huotari S. Temperature Dependence of the Near-Edge Spectrum of Water. J Phys Chem B 2011; 115:14544-50. [DOI: 10.1021/jp2015462] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tuomas Pylkkänen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- European Synchrotron Radiation Facility, B.P. 220, F-38043 Grenoble, France
| | - Arto Sakko
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Mikko Hakala
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Keijo Hämäläinen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Giulio Monaco
- European Synchrotron Radiation Facility, B.P. 220, F-38043 Grenoble, France
| | - Simo Huotari
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- European Synchrotron Radiation Facility, B.P. 220, F-38043 Grenoble, France
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48
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Huang C, Wikfeldt KT, Nordlund D, Bergmann U, McQueen T, Sellberg J, Pettersson LGM, Nilsson A. Wide-angle X-ray diffraction and molecular dynamics study of medium-range order in ambient and hot water. Phys Chem Chem Phys 2011; 13:19997-20007. [PMID: 22009343 DOI: 10.1039/c1cp22804h] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed wide-angle X-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 °C) under normal pressure. Using a spherically curved Ge crystal an energy resolution better than 15 eV has been achieved which eliminates influence from Compton scattering. The high quality of the data allows for a reliable Fourier transform of the experimental data resolving shell structure out to ~12 Å, i.e. 5 hydration shells. Large-scale molecular dynamics (MD) simulations using the TIP4P/2005 force-field reproduce excellently the experimental shell-structure in the range 4-12 Å although less agreement is seen for the first peak in the intermolecular pair-correlation function (PCF). The Shiratani-Sasai Local Structure Index [J. Chem. Phys. 104, 7671 (1996)] identifies a tetrahedral minority giving the intermediate-range oscillations in the O-O PCF and a disordered majority providing a more featureless background in this range. The current study supports the proposal that the structure of liquid water, even at high temperatures, can be described in terms of a two-state fluctuation model involving local structures related to the high-density and low-density forms of liquid water postulated in the liquid-liquid phase transition hypothesis.
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Affiliation(s)
- Congcong Huang
- Stanford Synchrotron Radiation Lightsource, Stanford, CA 94309, USA
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Temelso B, Archer KA, Shields GC. Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections. J Phys Chem A 2011; 115:12034-46. [DOI: 10.1021/jp2069489] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Kaye A. Archer
- Dean’s Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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